rs4088473

Variant names:

• chr11-63411679-A-G
• rs4088473

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.435 in 151,944 control chromosomes in the GnomAD database, including 16,690 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (16690 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65963 AN: 151826 Hom.: 16649 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.435

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.435 AC: 66077 AN: 151944 Hom.: 16690 Cov.: 31 AF XY: 0.436 AC XY: 32417 AN XY: 74274

African (AFR) AF: 0.651 AC: 26961 AN: 41426

American (AMR) AF: 0.485 AC: 7397 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 802 AN: 3464

East Asian (EAS) AF: 0.820 AC: 4234 AN: 5162

South Asian (SAS) AF: 0.486 AC: 2345 AN: 4824

European-Finnish (FIN) AF: 0.334 AC: 3523 AN: 10534

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19535 AN: 67974

Other (OTH) AF: 0.439 AC: 926 AN: 2108

Alfa AF: 0.370 Hom.: 1601

Bravo AF: 0.461

Asia WGS AF: 0.653 AC: 2248 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.035
DANN	Benign	0.48
PhyloP100		-0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4088473; hg19: chr11-63179151;